Can we use BIOLOG plates for accuracy?

draeger-lab / C_striatum_wetlab

This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs

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Can we use BIOLOG plates for accuracy? #1

Closed famosab closed 1 year ago

famosab commented 1 year ago

BIOLOG phenotype microarrays offer a fast way to access the metabolic potential of an organism: they test for various carbon, phosphorous, nitrogen and sulfur sources as well as for chemical sensitivities. Some studies¹ use these arrays to access model accuracy by comparison with GEM prediction.

There is a possibility to send the strains to BIOLOG and let them do the laboratory work. According to Simon, this will cost > 1000€. My plan is to ask them via Mail and see what quote they offer and how they would tackle the issue with small growth on defined media.

famosab commented 1 year ago

I asked for a custom protocol via form on the website today (19.10.2022).

famosab commented 1 year ago

I received an answer which was a bit inconclusive - It seems that they do not offer a service but we need to have the equipment on-site (which is very expensive). I will discuss this on Monday with Simon and Laura.

famosab commented 1 year ago

I will meet with Andre from BIOLOG on the 24.11.22 at 2pm UK time (3pm German time) to discuss my questions.

famosab commented 1 year ago

I looked into that: BIOLOG plates are rather expensive. While it might still be a nice way to access model accuracy, it is just not feasible at the moment for 4 strains and 3 biological replicates each.